[Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

Wed, Oct 5, 2016 11:58 AM

I just uploaded a fix.  This should be corrected in version 1.9.14


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Robert Castelo <robert.castelo at upf.edu>
Sent: Wednesday, October 5, 2016 1:00:21 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

hi,

there's a warning issued by GenomeInfoDb::keepStandardChromosomes()
because of multiple compatible sequence styles, that i guess it should
be corrected. this warning can be reproduced minimally as follows;

library(GenomicRanges)
library(GenomeInfoDb)

gr <- GRanges(seqnames="1", IRanges(1, 10))

gr <- keepStandardChromosomes(gr)
Warning message:
In if (!is.na(guess)) style <- unique(guess$style) else
return(dropSeqlevels(x,  :
   the condition has length > 1 and only the first element will be used

you can find the session info below. the specific line of code affected
on the lastest SVN version of GenomeInfoDb is:

keepStandardChromosomes <- function(x, species=NULL)
{
     ori_seqlevels <- seqlevels(x)
     if(!length(ori_seqlevels))
         return(x)

     ## guess at style
     guess <- .guessSpeciesStyle(ori_seqlevels)
     if (!is.na(guess))
         style <- unique(guess$style)
[...]


cheers,

robert.
ps: sessionInfo()
R Under development (unstable) (2016-05-04 r70581)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8
  [7] LC_PAPER=en_US.UTF8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices
[6] utils     datasets  methods   base

other attached packages:
[1] GenomicRanges_1.25.94 GenomeInfoDb_1.9.13
[3] IRanges_2.7.16        S4Vectors_0.11.17
[5] BiocGenerics_0.19.2   setwidth_1.0-4
[7] colorout_1.0-3

loaded via a namespace (and not attached):
[1] zlibbioc_1.19.0 XVector_0.13.7

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[Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

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